Where can I download single nucleus RNA-seq data from human cortex?

transcriptomics
how-to
rna-seq
atlas-cell-types
celltype

#1

Gene expression matrices and metadata can be downloaded here:
http://celltypes.brain-map.org/rnaseq

Matrices include exonic and intronic raw read counts with genes as rows and samples as columns. Gene and sample metadata are included as additional tables. Temporal cortex (MTG) data includes cell class and cluster labels and can be visualized here:
http://celltypes.brain-map.org/rnaseq/human
https://viewer.cytosplore.org/

Primary visual (V1) or anterior cingulate cortex (ACC) will include cluster annotations in the future.


#2

While currently cluster information is only available for a subset of mouse and human brain regions, class information (e.g., excitatory, inhibitory, non-neuronal) can be derived using the human (or mouse) RNA-Seq Data Navigator linked above. For example, by setting the “Set 1 selection” to all inhibitory cell types and setting the “Set 2 selection” to all excitatory types and running “Find Marker Genes”, we get the following gene lists:

  • Inhibitory cells: GAD1, SLC6A1, GAD2, GRIP2, DLX6-AS1, MAF, SLC24A3, LOC105375415, IGF1, ANK1
  • Excitatory cells: SLC17A7, SATB2, LOC105376407, NRGN, NPTX1, LY86-AS1, MLIP, SFTA1P, SV2B, KIAA1211L

Cells (or nuclei) in other brain regions which express most of these inhibitory markers are likely inhibitory, cells that express most the excitatory markers are likely excitatory, and cells that do not express these markers are likely non-neuronal or low quality.

Selecting marker genes for refinement to the subclass level or to specific non-neuronal populations could be done using a similar work flow.